Life/Bibliography

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Books

• Shubin, Neil (2013-01-08). The Universe Within: Discovering the Common History of Rocks, Planets, and People (p. 2)". Random House, Inc.. Kindle Edition.
  • "Inside every organ, cell, and piece of DNA in our bodies lie over 3.5 billion years of the history of life. Accordingly, clues to the human story reside within impressions of worms in rock, the DNA of fish, and clumps of algae in a pond…worms, fish, and algae are but gateways to ever deeper connections— ones that extend back billions of years before the presence of life and of Earth itself. Written inside us is the birth of the stars, the movement of heavenly bodies across the sky, even the origin of days themselves."

• Ashcroft FM. (2012) The spark of life: electricity in the human body. New York: Norton, ISBN 9780393078039. || Google Books preview. Chapters 1 & 2 previewed, with missing pages.
  • The history and contemporary story of the indispensable role of electricity within the human body, continual electrical signals throughout the body driving organ function and its manifestation as vision, locomotion, embryonic development, thinking—as remaining in the living state. | ”Frances Ashcroft is an award winning scientist, a professor of physiology at the University of Oxford, and a Fellow of both Trinity College Oxford and the Royal Society. The author of the international bestseller Life at the Extremes, she lives in Oxford".

• Schrödinger E. (1944, 2000) What is Life?: The Physical Aspect of the Living Cell; with, Mind and Matter; & Autobiographical Sketches. Foreword by Roger Penrose. Cambridge University Press (Canto). ISBN 0-521-42708-8 | Chapter 6: Order, Disorder and Entropy. | Google Books preview.
  • Prediction of hereditary molecule like a coded periodic crystal — Watson claims inspiration — Stresses open thermodynamic systems key to life.

• Rosen R. (1991) Life Itself: A Comprehensive Inquiry Into The Nature, Origin, And Fabrication Of Life. Columbia University Press, New York. ISBN 0-231-07565-0 | Google Books preview.
  • The question: "What is life?" is not often asked in biology, precisely because the machine metaphor already answers it: "Life is a machine." Indeed, to suggest otherwise is regarded as unscientific and viewed with the greatest hostility as an attempt to take biology back to metaphysics...This is the legacy of the machine metaphor. I hope to convince the reader, in the course of the present work, that the machine metaphor is not just a little bit wrong; it is entirely wrong and must be discarded.

• Kauffman SA. (1993) The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, New York. ISBN 0195058119

• Kauffman S. (1995) At Home in the Universe: The Search for Laws of Self-Organization and Complexity. Oxford University Press, New York. ISBN 0195095995

• Mayr E. (1997) Evolution and the Diversity of Life: Selected Essays. The Belknap Press of Harvard University Press, Cambridge, Massachusetts.

• Holland JH. (1998) Emergence: From Chaos to Order. Perseus Books, Cambridge. ISBN 0-7382-0142-1

• Hoagland M, Dodson B (1998) The Way Life Works: The Science Lovers Illustrated Guide to How Life Grows, Develops, Reproduces, and Gets Along. Three Rivers Press, New York ISBN 0-8129-2888-1 (For young people. An illustrated text.)

• Solé R, Goodwin B (2000) Signs of Life: How Complexity Pervades Biology. Basic Books, Perseus Books Group, New York ISBN 0-465-01928-5

• Loewenstein WR (2000) The Touchstone of life: Molecular Information, Cell Communication, and the Foundations of Life. Oxford University Press ISBN 0-19-514057-5 Book Review and Chapter One

• Margulis L, Sagan D. [Foreword by Niles Eldridge] (2000) What is Life? University of California Press. (pbk) ISBN 978-0-520-22021-8.
  • UC Press Description: Half a century ago, before the discovery of DNA, the Austrian physicist and philosopher Erwin Schrödinger inspired a generation of scientists by rephrasing the fascinating philosophical question: What is life?...[A]uthors Lynn Margulis and Dorion Sagan revisit this timeless question in a...narrative that combines rigorous science with philosophy, history, and poetry...from the dynamics of the bacterial realm, to the connection between sex and death, to theories of spirit and matter.
  • From inside flap hardcover edition: "In What Is Life? Margulis and Sagan have rephrased the answer to Schrödinger's brilliant question by means of a new and spirited explanation of the emergent levels of biological organization. . . . Theirs is a conceptual framework likely to influence future introductions to biology." --E. O. Wilson
  • Note: Google Books preview contains online full-text of Foreword and first 20 (of 32) pages of chapter 1.
• Hoagland M, Dodson B, Hauck J (2001) Exploring the Way Life Works: The Science of Biology. Jones and Bartlett Publishers, Inc, Mississauga, Ontario ISBN 0-7637-1688-X (For young people. An illustrated text.)

• Harold FM. (2001) The Way of the Cell: Molecules, Organisms, and the Order of Life. Oxford University Press, Oxford. ISBN 0195135121

• Keller EF. (2002) Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines. Cambridge, MA: Harvard University Press. ISBN 067400468. | Google Books preview.

• Buchanan M (2002) Nexus: Small Worlds and the Groundbreaking Science of Networks. W.W. Norton, New York ISBN 0-393-04153-0

• Dill KA, Bromberg S, Stigter D (2003) Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology. Garland Science, New York. ISBN 0-8153-2051-5

• Strogatz SH (2003) Sync: The Emerging Science of Spontaneous Order. Theia, New York ISBN 0-7868-6844-9

• De Duve C (2004) Life Evolving: Molecules, Mind, and Meaning. Oxford University Press. New York ISBN 0195156056

• Kirschner MW, Gerhart JC, Norton J. (2005) The Plausibility of Life: Resolving Darwin's Dilemma. Yale University Press, New Haven. ISBN 13-978-0-300-11977-0; 10-0-300-11977-1

• Kaneko K (2006) Life: An Introduction to Complex Systems Biology. Springer, Berlin ISBN 3-540-32666-9

• Reid RGB. (2007) Biological Emergences: Evolution by Natural Experiment. A Bradford Book, Cambridge . ISBN 10: 0-262-18257-2

• Haynie DT. (2008) Biological Thermodynamics. 2nd edition. Cambridge: Cambridge University Press. ISBN 9780521884464. | Google Books preview.
  • TOC: 1. Energy transformation | 2. The First Law of Thermodynamics | 3. The Second Law of Thermodynamics | 4. Gibbs free energy - theory | 5. Gibbs free energy - applications | 6. Statistical thermodynamics | 7. Binding equilibria | 8. Reaction kinetics | 9. The frontier of biological thermodynamics | 10. Appendices.

Articles

• Braakman R, Smith E. (2012) The Compositional and Evolutionary Logic of Metabolism (PDF). Working Paper. Santa Fe Institute.
  • The chemistry of life is distinguished by being both highly ordered and far from thermodynamic equilibrium [1].1 This dynamical order is maintained by the non-equilibrium transfer of electrons through the biosphere. Free energy from potential differences between electron donors and acceptors can be derived from a vari- ety of biogeochemical cycles [4], but within cells electron transfer is mediated by a small number of universal elec- tron carriers which drive a limited array of organic reactions [5]. Together these reactions make up metabolism, which governs the chemical dynamics both within organisms and across ecosystems. The universal and apparently conserved metabolic network transcends all known species diversification and evolutionary change [6, 7], and distinguishes the biosphere within the major classes of planetary processes.

• Theobald DL. (2010) A formal test of the theory of universal common ancestry. Nature 465(7295):219-222. PMID 20463738.
  • Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past...I test UCA by applying model selection theory to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.

• Nicholson WL (2009). Ancient micronauts: interplanetary transport of microbes by cosmic impacts. Trends Microbiol 17 (6): 243-50. PMID 19464895. Research Blogging. [e]
  • Abstract: Recent developments in microbiology, geophysics and planetary sciences raise the possibility that the planets in our solar system might not be biologically isolated. Hence, the possibility of lithopanspermia (the interplanetary transport of microbial passengers inside rocks) is presently being re-evaluated, with implications for the origin and evolution of life on Earth and within our solar system. Here, I summarize our current understanding of the physics of impacts, space transport of meteorites, and the potentiality of microorganisms to undergo and survive interplanetary transfer.

• Hulbert, A. J.; Reinald Pamplona & Rochelle Buffenstein et al. (2007), "Life and Death: Metabolic Rate, Membrane Composition, and Life Span of Animals", Physiological Reviews 87 (4): 1175-1213, DOI:10.1152/physrev.00047.2006 ^[e]
  • Abstract: Maximum life span differences among animal species exceed life span variation achieved by experimental manipulation by orders of magnitude. The differences in the characteristic maximum life span of species was initially proposed to be due to variation in mass-specific rate of metabolism. This is called the rate-of-living theory of aging and lies at the base of the oxidative-stress theory of aging, currently the most generally accepted explanation of aging. However, the rate-of-living theory of aging while helpful is not completely adequate in explaining the maximum life span. Recently, it has been discovered that the fatty acid composition of cell membranes varies systematically between species, and this underlies the variation in their metabolic rate. When combined with the fact that 1) the products of lipid peroxidation are powerful reactive molecular species, and 2) that fatty acids differ dramatically in their susceptibility to peroxidation, membrane fatty acid composition provides a mechanistic explanation of the variation in maximum life span among animal species. When the connection between metabolic rate and life span was first proposed a century ago, it was not known that membrane composition varies between species. Many of the exceptions to the rate-of-living theory appear explicable when the particular membrane fatty acid composition is considered for each case. Here we review the links between metabolic rate and maximum life span of mammals and birds as well as the linking role of membrane fatty acid composition in determining the maximum life span. The more limited information for ectothermic animals and treatments that extend life span (e.g., caloric restriction) are also reviewed.

• Epstein IR, Pojman JA, Steinbock O (2006) Introduction: Self-organization in nonequilibrium chemical systems. Chaos 16:037101 PMID 17014235
  • Abstract: The field of self-organization in nonequilibrium chemical systems comprises the study of dynamical phenomena in chemically reacting systems far from equilibrium. Systematic exploration of this area began with investigations of the temporal behavior of the Belousov-Zhabotinsky oscillating reaction, discovered accidentally in the former Soviet Union in the 1950s. The field soon advanced into chemical waves in excitable media and propagating fronts. With the systematic design of oscillating reactions in the 1980s and the discovery of Turing patterns in the 1990s, the scope of these studies expanded dramatically. The articles in this Focus Issue provide an overview of the development and current state of the field.

• Hazen R (2006) The Big Questions: What is Life? New Scientist Issue 2578, pages 46-51.
  • Excerpt: Scientists care about definitions, so they convene conferences to discuss the matter. A recent meeting called "What is life?" attracted a hundred scientists, who mingled with assorted philosophers and theologians to debate the issue. Opinions differed dramatically, but the most contentious debates occurred within the scientific ranks. One very senior expert on lipid molecules argued that life began with the first semi-permeable lipid membrane. An equally august authority on metabolism countered that life began with the first self-sustaining metabolic cycle. On the contrary, claimed several molecular biologists, the first living entity must have been an RNA-like genetic system that carried and duplicated biological information. One mineralogist even proposed the decidedly minority view that life began not as an organic entity, but as a self-replicating mineral.

• Marenduzzo D et al. (2006) Entropy-driven genome organization. Biophys J 90:3712-21 PMID 16500976
  • Abstract: DNA and RNA polymerases active on bacterial and human genomes in the crowded environment of a cell are modeled as beads spaced along a string. Aggregation of the large polymerizing complexes increases the entropy of the system through an increase in entropy of the many small crowding molecules; this occurs despite the entropic costs of looping the intervening DNA. Results of a quantitative cost/benefit analysis are consistent with observations that active polymerases cluster into replication and transcription “factories” in both pro- and eukaryotes. We conclude that the second law of thermodynamics acts through nonspecific entropic forces between engaged polymerases to drive the self-organization of genomes into loops containing several thousands (and sometimes millions) of basepairs.

• Morowitz H, Smith E (2006) Energy flow and the organization of life
  • Excerpt: The organization of energy flow through metabolic pathways allows us to recognize many forms of continuity absent in conventional thinking. We have good reason to believe that the first emergent metabolism was similar in many respects to modern universal core anabolism. Metabolism itself becomes a bridge from driven geochemistry to the foundations of cell physiology and trophic ecology. If our story is correct, the thermodynamic forces responsible for the emergence of anabolism within prebiotic chemistry have ensured its stability throughout the ensuing history of life. Energy flow embeds life within the geosphere not just mechanistically but conceptually as an inevitable form of driven geochemical order.

• Scheffer, M. & E. H. van Nes (2006), "Self-organized similarity, the evolutionary emergence of groups of similar species", Proceedings of the National Academy of Sciences 103 (16): 6230-6235, DOI:10.1073/pnas.0508024103 ^[e]
  • Abstract: Ecologists have long been puzzled by the fact that there are so many similar species in nature. Here we show that self-organized clusters of look-a-likes may emerge spontaneously from coevolution of competitors. The explanation is that there are two alternative ways to survive together: being sufficiently different or being sufficiently similar. Using a model based on classical competition theory, we demonstrate a tendency for evolutionary emergence of regularly spaced lumps of similar species along a niche axis. Indeed, such lumpy patterns are commonly observed in size distributions of organisms ranging from algae, zooplankton, and beetles to birds and mammals, and could not be well explained by earlier theory. Our results suggest that these patterns may represent self-constructed niches emerging from competitive interactions. A corollary of our findings is that, whereas in species-poor communities sympatric speciation and invasion of open niches is possible, species-saturated communities may be characterized by convergent evolution and invasion by look-a-likes.

• Walsh, D. (2006), "Organisms as natural purposes: the contemporary evolutionary perspective", Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 37: 771-791, DOI:10.1016/j.shpsc.2006.09.009 ^[e]
  • Abstract: Kant’s conception of organisms as natural purposes raises a challenge to the adequacy of mechanistic explanation in biology. Certain features of organisms appear to be inexplicable by appeal to mechanical law alone. Some biological phenomena, it seems, can only be accounted for teleologically. Contemporary evolutionary biology has by and large ignored this challenge. It is widely held that Darwin’s theory of natural selection gives us an adequate, wholly mechanical account of the nature of organisms. In contemporary biology, the category of the organism plays virtually no explanatory role. Contemporary evolutionary biology is a science of sub-organismal entities—replicators. I argue that recent advances in developmental biology demonstrate the inadequacy of sub-organismal mechanism. The category of the organism, construed as a ‘natural purpose’ should play an ineliminable role in explaining ontogenetic development and adaptive evolution. According to Kant the natural purposiveness of organisms cannot be demonstrated to be an objective principle in nature, nor can purposiveness figure in genuine explain. I attempt to argue, by appeal to recent work on self-organization, that the purposiveness of organisms is a natural phenomenon, and, by appeal to the apparatus of invariance explanation, that biological purposiveness provides genuine, ineliminable biological explanations.

• Park K et al. (2005) Self-organized scale-free networks. Phys Rev E Stat Nonlin Soft Matter Phys 72:026131 PMID 16196668

• Troisi A et al.(2005) An agent-based approach for modeling molecular self-organization. Proc Natl Acad Sci USA 102:255-60 PMID 15625108

• Pross, A. (2003), "The driving force for life's emergence: kinetic and thermodynamic considerations", J Theor Biol 220 (3): 393–406, DOI:10.1006/jtbi.2003.3178 ^[e]

• Koshland DE, Jr. (2002) Special essay. The seven pillars of life. Science 295:2215-2216 PMID 11910092
  • The Seven Pillars: Program (DNA), Improvisation (evolution), Compartmentalization (boundary with environment), Energy (the flow of energy through the system), Regeneration (re-synthesis of parts), Adaptability (‘behavioral’ responsiveness), Seclusion (metabolic pathways do not have their privacy invaded).

• Davis, B.K (2002), "Molecular evolution before the origin of species", Progress in biophysics and molecular biology 79 (1-3): 77–133, DOI:10.1016/S0079-6107(02)00012-3 ^[e]
• Pace NR (2001) Special Feature: The universal nature of biochemistry. Proc Natl Acad Sci USA 98:805-8
  
• Dronamraju KR (1999) Erwin Schrodinger and the origins of molecular biology. Genetics 153:1071-6 PMID 10545442
  • Excerpt: In What Is Life?, Schrödinger focused attention on two topics in biology: (a) the nature of the hereditary material and (b) the thermodynamics of living systems. In a review of the state of knowledge of genetics at that time,

Interviews and Commentaries

• Kauffman S. The Adjacent Possible: A Talk with Stuart Kauffman